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Fu J, Wang T, Xiao X, Cheng Y, Wang F, Jin M, Wang Y, Zong X. Clostridium Butyricum ZJU-F1 Benefits the Intestinal Barrier Function and Immune Response Associated with Its Modulation of Gut Microbiota in Weaned Piglets. Cells 2021; 10:cells10030527. [PMID: 33801396 PMCID: PMC8001369 DOI: 10.3390/cells10030527] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/23/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
This study investigated the effects of dietary C. butyricum ZJU-F1 on the apparent digestibility of nutrients, intestinal barrier function, immune response, and microflora of weaned piglets, with the aim of providing a theoretical basis for the application of Clostridium butyricum as an alternative to antibiotics in weaned piglets. A total of 120 weanling piglets were randomly divided into four treatment groups, in which piglets were fed a basal diet supplemented with antibiotics (CON), Bacillus licheniformis (BL), Clostridium butyricum ZJU-F1 (CB), or Clostridium butyricum and Bacillus licheniformis (CB-BL), respectively. The results showed that CB and CB-BL treatment increased the intestinal digestibility of nutrients, decreased intestinal permeability, and increased intestinal tight junction protein and mucin expression, thus maintaining the integrity of the intestinal epithelial barrier. CB and CB-BL, as exogenous probiotics, were also found to stimulate the immune response of weaned piglets and improve the expression of antimicrobial peptides in the ileum. In addition, dietary CB and CB-BL increased the proportion of Lactobacillus. The levels of butyric acid, propionic acid, acetic acid, and total acid were significantly increased in the ceca of piglets fed CB and CB-BL. Furthermore, we validated the effects of C. butyricum ZJU-F1 on the intestinal barrier function and immune response in vitro and found C. butyricum ZJU-F1 improved intestinal function and enhanced the TLR-2-MyD88-NF-κB signaling.
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Affiliation(s)
- Jie Fu
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.F.); (T.W.); (X.X.); (Y.C.); (F.W.); (M.J.)
| | - Tenghao Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.F.); (T.W.); (X.X.); (Y.C.); (F.W.); (M.J.)
| | - Xiao Xiao
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.F.); (T.W.); (X.X.); (Y.C.); (F.W.); (M.J.)
| | - Yuanzhi Cheng
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.F.); (T.W.); (X.X.); (Y.C.); (F.W.); (M.J.)
| | - Fengqin Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.F.); (T.W.); (X.X.); (Y.C.); (F.W.); (M.J.)
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingliang Jin
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.F.); (T.W.); (X.X.); (Y.C.); (F.W.); (M.J.)
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou 310058, China
| | - Yizhen Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.F.); (T.W.); (X.X.); (Y.C.); (F.W.); (M.J.)
- Correspondence: (Y.W.); (X.Z.)
| | - Xin Zong
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.F.); (T.W.); (X.X.); (Y.C.); (F.W.); (M.J.)
- Correspondence: (Y.W.); (X.Z.)
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152
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Jackrel SL, Yang JW, Schmidt KC, Denef VJ. Host specificity of microbiome assembly and its fitness effects in phytoplankton. THE ISME JOURNAL 2021; 15:774-788. [PMID: 33097853 PMCID: PMC8027036 DOI: 10.1038/s41396-020-00812-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/21/2022]
Abstract
Insights into symbiosis between eukaryotic hosts and their microbiomes have shifted paradigms on what determines host fitness, ecology, and behavior. Questions remain regarding the roles of host versus environment in shaping microbiomes, and how microbiome composition affects host fitness. Using a model system in ecology, phytoplankton, we tested whether microbiomes are host-specific, confer fitness benefits that are host-specific, and remain conserved in time in their composition and fitness effects. We used an experimental approach in which hosts were cleaned of bacteria and then exposed to bacterial communities from natural environments to permit recruitment of microbiomes. We found that phytoplankton microbiomes consisted of a subset of taxa recruited from these natural environments. Microbiome recruitment was host-specific, with host species explaining more variation in microbiome composition than environment. While microbiome composition shifted and then stabilized over time, host specificity remained for dozens of generations. Microbiomes increased host fitness, but these fitness effects were host-specific for only two of the five species. The shifts in microbiome composition over time amplified fitness benefits to the hosts. Overall, this work solidifies the importance of host factors in shaping microbiomes and elucidates the temporal dynamics of microbiome compositional and fitness effects.
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Affiliation(s)
- Sara L Jackrel
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
- Ecology, Behavior and Evolution Section, University of California San Diego, La Jolla, CA, USA.
| | - Jinny W Yang
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Kathryn C Schmidt
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent J Denef
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
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153
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Chen G. Editorial: Multimodal and Integrative Analysis of Single-Cell or Bulk Sequencing Data. Front Genet 2021; 12:658185. [PMID: 33719353 PMCID: PMC7952969 DOI: 10.3389/fgene.2021.658185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/08/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Geng Chen
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Genecast Biotechnology Co., Ltd., Wuxi, China
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154
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Kundu P, Torres ERS, Stagaman K, Kasschau K, Okhovat M, Holden S, Ward S, Nevonen KA, Davis BA, Saito T, Saido TC, Carbone L, Sharpton TJ, Raber J. Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in App NL-G-F, App NL-F, and wild type mice. Sci Rep 2021; 11:4678. [PMID: 33633159 PMCID: PMC7907263 DOI: 10.1038/s41598-021-83851-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetic mechanisms occurring in the brain as well as alterations in the gut microbiome composition might contribute to Alzheimer’s disease (AD). Human amyloid precursor protein knock-in (KI) mice contain the Swedish and Iberian mutations (AppNL-F) or those two and also the Arctic mutation (AppNL-G-F). In this study, we assessed whether behavioral and cognitive performance in 6-month-old AppNL-F, AppNL-G-F, and C57BL/6J wild-type (WT) mice was associated with the gut microbiome, and whether the genotype modulates this association. The genotype effects observed in behavioral tests were test-dependent. The biodiversity and composition of the gut microbiome linked to various aspects of mouse behavioral and cognitive performance but differences in genotype modulated these relationships. These genotype-dependent associations include members of the Lachnospiraceae and Ruminococcaceae families. In a subset of female mice, we assessed DNA methylation in the hippocampus and investigated whether alterations in hippocampal DNA methylation were associated with the gut microbiome. Among other differentially methylated regions, we identified a 1 Kb region that overlapped ing 3′UTR of the Tomm40 gene and the promoter region of the Apoe gene that and was significantly more methylated in the hippocampus of AppNL-G-F than WT mice. The integrated gut microbiome hippocampal DNA methylation analysis revealed a positive relationship between amplicon sequence variants (ASVs) within the Lachnospiraceae family and methylation at the Apoe gene. Hence, these microbes may elicit an impact on AD-relevant behavioral and cognitive performance via epigenetic changes in AD-susceptibility genes in neural tissue or that such changes in the epigenome can elicit alterations in intestinal physiology that affect the growth of these taxa in the gut microbiome.
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Affiliation(s)
- Payel Kundu
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eileen Ruth S Torres
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Kristin Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Sarah Holden
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Samantha Ward
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Brett A Davis
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA.,Departments of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA.,Departments of Medical Informatics and Clinical Epidemiology, Portland, OR, 97239, USA.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA.,Department of Statistics, Oregon State University, Corvallis, OR, 97331, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA. .,Departments of Neurology, Psychiatry, and Radiation Medicine, Division of Neuroscience ONPRC, Oregon Health & Science University, Portland, OR, 97239, USA. .,College of Pharmacy, Oregon State University, Corvallis, OR, 97331, USA. .,Department of Behavioral Neuroscience, L470, Oregon Health & Science University, 3181SW Sam Jackson Park Road, Portland, OR, 97239, USA.
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155
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Nikouli E, Meziti A, Smeti E, Antonopoulou E, Mente E, Kormas KA. Gut Microbiota of Five Sympatrically Farmed Marine Fish Species in the Aegean Sea. MICROBIAL ECOLOGY 2021; 81:460-470. [PMID: 32840670 DOI: 10.1007/s00248-020-01580-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
In this study, we hypothesized that sympatrically grown farmed fish, i.e. fish which experience similar environmental conditions and nutritionally similar diets, would have more convergent gut microbiota. Using a "common garden" approach, we identified the core microbiota and bacterial community structure differences between five fish species farmed in the same aquaculture site on the west coast of the Aegean Sea, Greece. The investigated individuals were at similar developmental stages and reared in adjacent (< 50 m) aquaculture cages; each cage had 15 kg fish m-3. The diets were nutritionally similar to support optimal growth for each fish species. DNA from the midgut of 3-6 individuals per fish species was extracted and sequenced for the V3-V4 region of the bacterial 16S rRNA. Only 3.9% of the total 181 operational taxonomic units (OTUs) were shared among all fish. Between 5 and 74 OTUs were unique to each fish species. Each of the investigated fish species had a distinct profile of dominant OTUs, i.e. cumulative relative abundance of ≥ 80%. Co-occurrence network analysis for each fish species showed that all networks were strongly dominated by positive correlations between the abundances of their OTUs. However, each fish species had different network characteristics suggesting the differential significance of the OTUs in each of the five fish species midgut. The results of the present study may provide evidence that adult fish farmed in the Mediterranean Sea have a rather divergent and species-specific gut microbiota profile, which are shaped independently of the similar environmental conditions under which they grow.
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Affiliation(s)
- Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Evangelia Smeti
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research (HCMR), 46.7km Athens-Sounio Ave., Anavyssos, 19013, Athens, Greece
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Konstantinos Ar Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece.
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156
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Wang Y, Cheng H, Chang F, Zhao L, Wang B, Wan Y, Yue M. Endosphere Microbiome and Metabolic Differences Between the Spots and Green Parts of Tricyrtis macropoda Leaves. Front Microbiol 2021; 11:599829. [PMID: 33505373 PMCID: PMC7829350 DOI: 10.3389/fmicb.2020.599829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022] Open
Abstract
Background Plant leaves are important organs for photosynthesis and biological energy production. The leaves of Tricyrtis macropoda have an unusual spotted pattern. However, whether the spots of T. macropoda affect the plant microbiome and metabolites is unclear. In this study, we compared differences in the endosphere microbiome and plant metabolites in green parts and spots and the effects of spots on the photosynthesis of leaves. Methods 16S/ITS sequences and metabolite spectra were obtained by high-throughput amplicon sequencing and ultra-high-performance liquid chromatography–high-resolution mass spectrometry, respectively. Changes in the diversity of the endophytic microbial community and metabolites were studied, and the effect of T. macropoda leaf spots on photosynthesis was examined by chlorophyll fluorescence. Results The results showed that the relative abundance of Cercospora fungi in the leaf spots of T. macropoda was significantly higher than that in the green parts (P < 0.05) while Colletotrichum fungi showed low abundance in the spots. Alkaloid and ketone metabolites were decreased in the green parts compared with the spots, and amino acids, organic acids, lipids, and other compounds were increased in the green parts compared with the spots. A combined analysis of microbial communities and metabolites showed a significant correlation between the endophytic fungal communities and metabolite production. The changes in these metabolites may cause changes in local leaf color. In addition, we found that the spot areas of T. macropoda can be photosynthetically normal. Conclusion This research showed the relationship between endophytic microorganisms and metabolites, and the findings advance our understanding of endophyte–plant interactions and provide a new direction for investigating the relationship between endophytes and phenotypes.
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Affiliation(s)
- Yan Wang
- Microbiology Institute of Shaanxi, Xi'an, China
| | - Huyin Cheng
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Fan Chang
- Microbiology Institute of Shaanxi, Xi'an, China
| | - Le Zhao
- School of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Bin Wang
- College of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, China
| | - Yi Wan
- Microbiology Institute of Shaanxi, Xi'an, China
| | - Ming Yue
- School of Life Sciences, Northwest University, Xi'an, China
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157
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Oyola MG, Johnson RC, Bauman BM, Frey KG, Russell AL, Cho‐Clark M, Buban KN, Bishop‐Lilly KA, Merrell DS, Handa RJ, Wu TJ. Gut microbiota and metabolic marker alteration following dietary isoflavone-photoperiod interaction. Endocrinol Diabetes Metab 2021; 4:e00190. [PMID: 33532621 PMCID: PMC7831223 DOI: 10.1002/edm2.190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/09/2020] [Accepted: 09/12/2020] [Indexed: 11/06/2022] Open
Abstract
Introduction The interaction between isoflavones and the gut microbiota has been highlighted as a potential regulator of obesity and diabetes. In this study, we examined the interaction between isoflavones and a shortened activity photoperiod on the gut microbiome. Methods Male mice were exposed to a diet containing no isoflavones (NIF) or a regular diet (RD) containing the usual isoflavones level found in a standard vivarium chow. These groups were further divided into regular (12L:12D) or short active (16L:8D) photoperiod, which mimics seasonal changes observed at high latitudes. White adipose tissue and genes involved in lipid metabolism and adipogenesis processes were analysed. Bacterial genomic DNA was isolated from fecal boli, and 16S ribosomal RNA sequencing was performed. Results NIF diet increased body weight and adipocyte size when compared to mice on RD. The lack of isoflavones and photoperiod alteration also caused dysregulation of lipoprotein lipase (Lpl), glucose transporter type 4 (Glut-4) and peroxisome proliferator-activated receptor gamma (Pparg) genes. Using 16S ribosomal RNA sequencing, we found that mice fed the NIF diet had a greater proportion of Firmicutes than Bacteroidetes when compared to animals on the RD. These alterations were accompanied by changes in the endocrine profile, with lower thyroid-stimulating hormone levels in the NIF group compared to the RD. Interestingly, the NIF group displayed increased locomotion as compared to the RD group. Conclusion Together, these data show an interaction between the gut bacterial communities, photoperiod length and isoflavone compounds, which may be essential for understanding and improving metabolic health.
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Affiliation(s)
- Mario G. Oyola
- Department of Obstetrics and GynecologyUniformed Services University of the Health SciencesBethesdaMDUSA
- Center for Neuroscience and Regenerative MedicineUniformed Services University of the Health SciencesBethesdaMDUSA
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Ryan C. Johnson
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Bradly M. Bauman
- Department of Obstetrics and GynecologyUniformed Services University of the Health SciencesBethesdaMDUSA
| | - Kenneth G. Frey
- Genomics and Bioinformatics DepartmentBiological Defense Research DirectorateNaval Medical Research Center – FrederickFort DetrickMDUSA
| | - Ashley L. Russell
- Department of Obstetrics and GynecologyUniformed Services University of the Health SciencesBethesdaMDUSA
- Center for Neuroscience and Regenerative MedicineUniformed Services University of the Health SciencesBethesdaMDUSA
| | - Madelaine Cho‐Clark
- Department of Obstetrics and GynecologyUniformed Services University of the Health SciencesBethesdaMDUSA
| | - Katelyn N. Buban
- Department of Obstetrics and GynecologyUniformed Services University of the Health SciencesBethesdaMDUSA
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMDUSA
| | - Kimberly A. Bishop‐Lilly
- Genomics and Bioinformatics DepartmentBiological Defense Research DirectorateNaval Medical Research Center – FrederickFort DetrickMDUSA
- Program in Emerging Infectious DiseasesUniformed Services University of the Health SciencesBethesdaMDUSA
| | - D. Scott Merrell
- Program in Emerging Infectious DiseasesUniformed Services University of the Health SciencesBethesdaMDUSA
- Department of Microbiology and ImmunologyUniformed Services University of the Health SciencesBethesdaMDUSA
| | - Robert J. Handa
- Department of Biomedical SciencesColorado State UniversityFort CollinsCOUSA
| | - T. John Wu
- Department of Obstetrics and GynecologyUniformed Services University of the Health SciencesBethesdaMDUSA
- Center for Neuroscience and Regenerative MedicineUniformed Services University of the Health SciencesBethesdaMDUSA
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158
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Qian H, Zhang Q, Lu T, Peijnenburg WJGM, Penuelas J, Zhu YG. Lessons learned from COVID-19 on potentially pathogenic soil microorganisms. SOIL ECOLOGY LETTERS 2021. [PMCID: PMC7661327 DOI: 10.1007/s42832-020-0068-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 China
| | - W. J. G. M. Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, The Netherlands
- Center for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven, The Netherlands
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, 08193 Barcelona, Catalonia Spain
- CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia Spain
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085 China
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159
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Suppa A, Kvist J, Li X, Dhandapani V, Almulla H, Tian AY, Kissane S, Zhou J, Perotti A, Mangelson H, Langford K, Rossi V, Brown JB, Orsini L. Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species. MICROBIOME 2020; 8:170. [PMID: 33339542 PMCID: PMC7780628 DOI: 10.1186/s40168-020-00943-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 11/09/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. RESULTS We demonstrate that chronic exposure to ecologically relevant concentrations of glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, induce significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the "Reactome," we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways, and collagen degradation, responsible for the repair of wounds and tissue remodeling. CONCLUSIONS Our results show that chronic exposure to concentrations of Roundup and glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services. Video Abstract.
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Affiliation(s)
- Antonio Suppa
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
- Department of Chemistry, Life Sciences and Environmental Sustainability University of Parma, Department of Life Sciences, Viale Usberti, 11/A, Parma, Italy
| | - Jouni Kvist
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Vignesh Dhandapani
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Hanan Almulla
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | | | - Stephen Kissane
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Jiarui Zhou
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Alessio Perotti
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | | | | | - Valeria Rossi
- Department of Chemistry, Life Sciences and Environmental Sustainability University of Parma, Department of Life Sciences, Viale Usberti, 11/A, Parma, Italy
| | - James B. Brown
- Environmental Bioinformatics, Centre for Computational Biology, School of Biosciences, University of Birmingham Edgbaston, Birmingham, B15 2TT UK
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Statistics Department, University of California, Berkeley, Berkeley, CA, 94720 USA, Preminon LLC, Rodeo, CA 94572 USA
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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Liu D, Herrera M, Yu F, Pèrez-Moreno J. Provenances originate morphological and microbiome variation of Tuber pseudobrumale in southwestern China despite strong genetic consistency. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01645-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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161
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Torres Luque A, Fontana C, Pasteris SE, Bassi D, Cocconcelli PS, Otero MC. Bacterial communities associated to the urethra of healthy gilts and pregnant sows undergoing different reproductive protocols. J Anim Sci 2020; 98:5890613. [PMID: 32777034 DOI: 10.1093/jas/skaa258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022] Open
Abstract
Nowadays, it is known that the urogenital microbiota plays a key role in the urinary health of mammalians. Despite the urinary infections affect the health and the welfare of breeding sows, the urethral microbiota of healthy sows remains unknown. Therefore, this work evaluates the urethral bacterial communities of healthy gilts and sows to determine the presence of Enterobacteriaceae populations, and the structure of this microbiota in gilts (G) and pregnant (P) sows. Samples were collected by scraping the urethral mucosa of G (n = 9) and P sows, which included natural mating (NM, n = 9) and artificial inseminated (AI, n = 7) sows. Samples were analyzed by culture-dependent techniques and 16S-rRNA gene high-throughput-sequencing. All females were positive for Enterobacteriaceae culture, without significant differences (Kruskal-Wallis) between G and P groups (median values: 2.78 and 3.09 log CFU/mL, respectively; P = 0.497). Also, the rate of Enterobacteriaceae/total mesophilic microorganisms was individually calculated, without significant differences between G and P sows (median values: 0.61 and 0.66, respectively; P = 0.497). When analyzing the bacterial communities, it was found similar richness in G, NM, and AI; however, diversity was lower in P sows than G (Mann Whitney/Kruskal-Wallis test, P < 0.01). The dominating phyla that constituted a "core microbiome" included Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, which were common for all the studied females. The relative abundance for phyla, families, and genera was estimated, and Firmicutes was significantly higher in NM than AI sows (P = 0.02, Mann-Whitney/Kruskal Wallis test for univariate statistical comparisons); Pseudomonadaceae and Enterobacteriaceae were higher in AI than in NM (Mann-Whitney/Kruskal-Wallis, P < 0.05). Lactobacillus and Pseudomonas were among the dominant genera; however, only Pseudomonas sp. was significantly higher in AI than NM (Mann-Whitney/Kruskal-Wallis, P = 0.006). The results represent the first evidence about the existence of a urethral microbiota that includes Enterobacteriaceae, as well as the patterns of this microbiota in G and P sows. The knowledge of this urethral microbiota might allow for future research to develop innovative protocols to restore and/or preserve the healthy ecology of the urinary microbiome to prevent diseases ensuring the welfare of breeding sows.
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Affiliation(s)
- Andrea Torres Luque
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, San Miguel de Tucumán, Argentina
| | - Cecilia Fontana
- Estación Experimental Agropecuaria Famaillá INTA, Famaillá, Tucumán, Argentina
| | - Sergio E Pasteris
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, San Miguel de Tucumán, Argentina
| | - Daniela Bassi
- Dipartimento di Scienze e Tecnologie Alimentari per una filiera agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy
| | - Pier S Cocconcelli
- Dipartimento di Scienze e Tecnologie Alimentari per una filiera agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy
| | - María C Otero
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, San Miguel de Tucumán, Argentina
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162
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Aguirre de Cárcer D. Experimental and computational approaches to unravel microbial community assembly. Comput Struct Biotechnol J 2020; 18:4071-4081. [PMID: 33363703 PMCID: PMC7736701 DOI: 10.1016/j.csbj.2020.11.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.
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163
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Wu X, Shang Y, Wei Q, Chen J, Zhang H, Chen Y, Gao X, Wang Z, Zhang H. Gut Microbiota in Dholes During Estrus. Front Microbiol 2020; 11:575731. [PMID: 33329438 PMCID: PMC7734286 DOI: 10.3389/fmicb.2020.575731] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
The co-evolution of gut microbes and the host plays a vital role in the survival and reproduction of the host. The dhole (Cuon alpinus) has been listed as endangered species by the International Union for Conservation of Nature; therefore, conservation and effective breeding of dholes are essential. Effective estrus can promote reproduction. However, little is known about the relative contribution of estrus in shaping the structure and the functions of fecal microbiota. Here, we investigated the potential association between estrus and the fecal microbiota in dholes using shotgun metagenomic sequencing. We found that the estrus stages in dholes vary significantly in terms of gut bacterial composition and microbiome metabolism and function. Compared with that of non-estrus, adult dholes, the microbiome of estrus adult dholes had a significantly higher abundance of Bacillus faecalis and Veillonella, which play a key role in the synthesis of sex hormones and nucleic acids, energy production, and reproductive cell division. The insulin and energy metabolism-related pathways are significantly enhanced in the gut microbes and the related gluconeogenic enzymes are significantly enriched during estrus. These findings suggest that the structure and metagenome of the fecal microbiome during estrus have a significant effect in promoting estrus in dholes, thus providing a new perspective for dhole conservation.
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Affiliation(s)
- Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaodong Gao
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Zhiyong Wang
- Shijiazhuang Wildlife Conservation Center, Shijiazhuang, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, China
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164
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Pan ZY, Chang YX, Han N, Hou FY, Lee BJY, Zhi FC, Yang RF, Bi YJ. Short-term high-dose gavage of hydroxychloroquine changes gut microbiota but not the intestinal integrity and immunological responses in mice. Life Sci 2020; 264:118450. [PMID: 33131749 PMCID: PMC7578705 DOI: 10.1016/j.lfs.2020.118450] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/13/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022]
Abstract
Aims Hydroxychloroquine (HCQ), a widely used antimalarial drug, is proposed to treat coronavirus disease 2019 (COVID-19). However, no report is currently available regarding the direct effects of HCQ on gut microbiota, which is associated with the outcomes of elderly patients with COVID-19. Here, we first investigated the effects of HCQ on intestinal microecology in mice. Main methods Fifteen female C57BL/6J mice were randomly divided into two groups: HCQ group (n = 10) and control group (n = 5). Mice in the HCQ group were administered with HCQ at dose of 100 mg/kg by gavage daily for 14 days. The feces of mice were collected before and on the 7th and 14th days after HCQ challenge, and then analyzed by 16S rRNA amplicon sequencing. At the end of the experiment, the hematology, serum biochemistry and cytokines were determined, respectively. The mRNA expression of tight junction proteins in colonic tissues were also studied by RT-PCR. Key findings HCQ challenge had no effects on the counts of white blood cells, the levels of serum cytokines, and the gene expression of tight junction proteins in colon. HCQ also did not increase the content of serum d-lactate in mice. Notably, HCQ significantly decreased the diversity of gut microbiota, increased the relative abundance of phylum Bacteroidetes whereas decreased that of Firmicutes. Significance Short-term high dose HCQ challenge changes gut microbiota but not the intestinal integrity and immunological responses in mice. Special attention should be paid to the effects of HCQ on intestinal microecology in future clinical use.
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Affiliation(s)
- Zhi-Yuan Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Yu-Xiao Chang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Ni Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Feng-Yi Hou
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - B J Yang Lee
- Beijing Future Science & Technology Development Co., Ltd., Beijing, PR China
| | - Fa-Chao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Rui-Fu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Yu-Jing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China.
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165
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Xu F, Fu Y, Sun TY, Jiang Z, Miao Z, Shuai M, Gou W, Ling CW, Yang J, Wang J, Chen YM, Zheng JS. The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases. MICROBIOME 2020; 8:145. [PMID: 33032658 PMCID: PMC7545574 DOI: 10.1186/s40168-020-00923-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/13/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct microbiome features among complex human diseases remain largely unclear. RESULTS This analysis was based on a Chinese population with 1475 participants. We estimated the SNP-based heritability, which suggested that Desulfovibrionaceae and Odoribacter had significant heritability estimates (0.456 and 0.476, respectively). We performed a microbiome genome-wide association study to identify host genetic variants associated with the gut microbiome. We then conducted bidirectional Mendelian randomization analyses to examine the potential causal associations between the gut microbiome and complex human diseases. We found that Saccharibacteria could potentially decrease the concentration of serum creatinine and increase the estimated glomerular filtration rate. On the other hand, atrial fibrillation, chronic kidney disease and prostate cancer, as predicted by host genetics, had potential causal effects on the abundance of some specific gut microbiota. For example, atrial fibrillation increased the abundance of Burkholderiales and Alcaligenaceae and decreased the abundance of Lachnobacterium, Bacteroides coprophilus, Barnesiellaceae, an undefined genus in the family Veillonellaceae and Mitsuokella. Further disease-microbiome feature analysis suggested that systemic lupus erythematosus and chronic myeloid leukaemia shared common gut microbiome features. CONCLUSIONS These results suggest that different complex human diseases share common and distinct gut microbiome features, which may help reshape our understanding of disease aetiology in humans. Video Abstract.
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Affiliation(s)
- Fengzhe Xu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yuanqing Fu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Ting-Yu Sun
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zengliang Jiang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Zelei Miao
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Menglei Shuai
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Wanglong Gou
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Chu-Wen Ling
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, QLD, Brisbane, Australia
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jun Wang
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yu-Ming Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
| | - Ju-Sheng Zheng
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
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166
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Panteli N, Mastoraki M, Nikouli E, Lazarina M, Antonopoulou E, Kormas KA. Imprinting statistically sound conclusions for gut microbiota in comparative animal studies: A case study with diet and teleost fishes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100738. [PMID: 32896688 DOI: 10.1016/j.cbd.2020.100738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Despite the technical progress in high-throughput sequencing technologies, defining the sample size which is capable of yielding representative inferences in metabarcoding analysis still remains debatable. The present study addresses the influence of individual variability in assessing dietary effects on fish gut microbiota parameters and estimates the biological sample size that is sufficient to imprint a statistically secure outcome. European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata) were fed three alternative animal protein diets and a fishmeal control diet. Gut microbiota data from 12 individuals per diet, derived from Illumina sequencing of the V3-V4 region of the 16S rRNA gene, were randomized in all possible combinations of n-1 individuals. Results in this study showcased that increasing the sample size can limit the prevalence of individuals with high microbial load on the outcome and can ensure the statistical confidence required for an accurate validation of dietary-induced microbe shifts. Inter-individual variability was evident in the four dietary treatments where consequently misleading inferences arose from insufficient biological replication. These findings have critical implications for the design of future metabarcoding studies and highlight the urgency in selecting an adequate sample size able to safely elucidate the dietary effects on fish gut microbial communities.
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Affiliation(s)
- Nikolas Panteli
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Maria Mastoraki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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167
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Liu T, Liang X, Lei C, Huang Q, Song W, Fang R, Li C, Li X, Mo H, Sun N, Lv H, Liu Z. High-Fat Diet Affects Heavy Metal Accumulation and Toxicity to Mice Liver and Kidney Probably via Gut Microbiota. Front Microbiol 2020; 11:1604. [PMID: 32849333 PMCID: PMC7399142 DOI: 10.3389/fmicb.2020.01604] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 06/18/2020] [Indexed: 11/13/2022] Open
Abstract
Previous studies proved that heavy metals could increase the risk of disease by acting on the gut microbiota. Meanwhile, gut microbiota played important roles in detoxifying heavy metals. However, the response of gut microbiota to heavy metals and which microbes dominated this detoxification processes are still unclear. This study investigated the difference of high-fat-diet (HFD) and normal-diet (ND) gut microbiota and their response to and detoxification effects on arsenic (As), cadmium (Cd), and lead (Pb) exposure. Results showed that gut microbiota of ND and HFD was significantly different and responded to As, Pb, and Cd exposure differently, too. When exposed to 100 ppm As, Cd, or Pb, HFD-fed mice accumulated more heavy metals in the liver and kidney along with more severe functional damage than ND-fed mice, indicated by a more dramatic increase of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities and urinary total protein (TPU), urinary uric acid (UUA), and urinary creatinine (Ucrea) content. Among ND gut microbiota, relative abundance of Bacteroides, Lactobacillus, Butyricimonas, and Dorea was significantly increased by arsenic (As) exposure; relative abundance of Faecoccus and Lactobacillus was significantly increased by Cd exposure; relative abundance of Desulfovibrio, Plasmodium, and Roseburia were significantly increased by Pb exposure. However, among HFD gut microbiota, those microbes were not significantly changed. Bivariate association analysis found weak positive correlations between content of fecal excreted heavy metals and richness of total fecal microbiota as well as abundance of some of the heavy metal-enriched microbes. Our study concluded that HFD increased disease risk of heavy metal exposure probably via its gut microbiota which excreted less heavy metal through feces.
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Affiliation(s)
- Ting Liu
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xue Liang
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chao Lei
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qinhong Huang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weiqi Song
- Department of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Rong Fang
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chen Li
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaomei Li
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui Mo
- The Public Laboratory, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ning Sun
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Research Institute of Chinese Medicine Sciences, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haoran Lv
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhihua Liu
- Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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168
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Ye M, Yu J, Shi X, Zhu J, Gao X, Liu W. Polysaccharides catabolism by the human gut bacterium - Bacteroides thetaiotaomicron: advances and perspectives. Crit Rev Food Sci Nutr 2020; 61:3569-3588. [PMID: 32779480 DOI: 10.1080/10408398.2020.1803198] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, the degradation processes of polysaccharides by human gut microbiota are receiving considerable attention due to the discoveries of the powerful function of gut microbiota. Gut microbiota has developed a sensitive, accurate, and complex system for sensing, capturing, and degrading different polysaccharides. Among the gut microbiota, Bacteroides thetaiotaomicron, a representative species of Bacteroides, is considered as the best degrader of polysaccharides and a potential probiotic in pharmaceutical and food industries. Here, we summarize the degradation system of B. thetaiotaomicron and the degradation pathways of different polysaccharides by B. thetaiotaomicron. We also describe a technical route for investigating a specific polysaccharide degradation pathway by human gut bacteria. In addition, we also provide the future perspectives in the development of novel polysaccharides or oligosaccharides drugs, precision microbiology medicine, and personalized nutrition.
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Affiliation(s)
- Meng Ye
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Juping Yu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Xuexia Shi
- Department of Clinical Pharmacy, Qinghai University Affiliated Hospital, Xining, PR China
| | - Jingyi Zhu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Wei Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China.,Department of Clinical Pharmacy, Qinghai University Affiliated Hospital, Xining, PR China
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169
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Bacterial Peptidoglycans from Microbiota in Neurodevelopment and Behavior. Trends Mol Med 2020; 26:729-743. [DOI: 10.1016/j.molmed.2020.05.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/05/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023]
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170
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Zhu T, Duan YY, Kong FQ, Galzote C, Quan ZX. Dynamics of Skin Mycobiome in Infants. Front Microbiol 2020; 11:1790. [PMID: 32849406 PMCID: PMC7401610 DOI: 10.3389/fmicb.2020.01790] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/08/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the microbial community structure of the human skin is important for treating cutaneous diseases; however, little is known regarding skin fungal communities (mycobiomes). The aim of the present study was to investigate the features of and variations in skin fungal communities during infancy in 110 subjects less than 6 months of age. Skin samples were obtained from the back, antecubital fossa, and volar forearm, while physiological parameters including transepidermal water loss, pH, surface moisture, and deep layer hydration were evaluated. Skin fungal diversity decreased after the first three months of life. Differences in fungal community composition were greater among individual infants than among the three skin sites in the same individual. Inter- and intra-individual variation were similar and lower, respectively, than the variability between two samples obtained 12 weeks apart, from the same site in the same subject, suggesting low stability of fungal communities on infant skin. Skin physiological parameters showed little correlation with skin fungal community structure. Additionally, Malassezia was the most represented genus (36.43%) and M. globosa was the most abundant species in Malassezia with its abundance decreasing from 54.06% at 0–2 months to 34.54% at 5–6 months. These findings provide a basis for investigating the causative fungi-skin interactions associated with skin diseases.
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Affiliation(s)
- Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuan-Yuan Duan
- AP Skin Testing Center, Johnson & Johnson China Ltd., Shanghai, China
| | - Fan-Qi Kong
- AP Skin Testing Center, Johnson & Johnson China Ltd., Shanghai, China
| | - Carlos Galzote
- Johnson & Johnson International (Singapore) Pte. Ltd., Manila, Philippines
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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171
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Affiliation(s)
- Ajit Singh
- Department of Veterinary Microbiology, Lajpat Rai University of Veterinary and Animal Sciences, Hisar-125004, India
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172
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Egan S, Fukatsu T, Francino MP. Opportunities and Challenges to Microbial Symbiosis Research in the Microbiome Era. Front Microbiol 2020; 11:1150. [PMID: 32612581 PMCID: PMC7308722 DOI: 10.3389/fmicb.2020.01150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/06/2020] [Indexed: 01/04/2023] Open
Affiliation(s)
- Suhelen Egan
- Centre for Marine Science and Innovation (CMSI), School of Biological, Earth and Environmental Sciences (BEES), UNSW Sydney, Sydney, NSW, Australia
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - M Pilar Francino
- Joint Research Unit in Genomics and Health, Fundació per al Foment de la Investigació Sanitária i Biomèdica de la Comunitat Valenciana (FISABIO)/Institut de Biologia Integrativa de Sistemes (Universitat de València i Consejo Superior de Investigaciones Científicas), València, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain
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Abstract
The interplay between the commensal microbiota and the mammalian immune system development and function includes multifold interactions in homeostasis and disease. The microbiome plays critical roles in the training and development of major components of the host's innate and adaptive immune system, while the immune system orchestrates the maintenance of key features of host-microbe symbiosis. In a genetically susceptible host, imbalances in microbiota-immunity interactions under defined environmental contexts are believed to contribute to the pathogenesis of a multitude of immune-mediated disorders. Here, we review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs. We highlight aspects of the current knowledge, challenges and limitations in achieving causal understanding of host immune-microbiome interactions, as well as their impact on immune-mediated diseases, and discuss how these insights may translate towards future development of microbiome-targeted therapeutic interventions.
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174
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Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res 2020; 30:492-506. [PMID: 32433595 PMCID: PMC7264227 DOI: 10.1038/s41422-020-0332-7] [Citation(s) in RCA: 2125] [Impact Index Per Article: 425.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/20/2020] [Indexed: 02/08/2023] Open
Abstract
The interplay between the commensal microbiota and the mammalian immune system development and function includes multifold interactions in homeostasis and disease. The microbiome plays critical roles in the training and development of major components of the host's innate and adaptive immune system, while the immune system orchestrates the maintenance of key features of host-microbe symbiosis. In a genetically susceptible host, imbalances in microbiota-immunity interactions under defined environmental contexts are believed to contribute to the pathogenesis of a multitude of immune-mediated disorders. Here, we review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs. We highlight aspects of the current knowledge, challenges and limitations in achieving causal understanding of host immune-microbiome interactions, as well as their impact on immune-mediated diseases, and discuss how these insights may translate towards future development of microbiome-targeted therapeutic interventions.
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Affiliation(s)
- Danping Zheng
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel.,Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Timur Liwinski
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel.,1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel. .,Cancer-Microbiome Division, Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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175
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Jorge F, Dheilly NM, Poulin R. Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite. Front Microbiol 2020; 11:954. [PMID: 32508779 PMCID: PMC7248275 DOI: 10.3389/fmicb.2020.00954] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022] Open
Abstract
Animal microbiomes influence their development, behavior and interactions with other organisms. Parasitic metazoans also harbor microbial communities; although they are likely to modulate host-parasite interactions, little is known about parasite microbiomes. The persistence of microbial communities throughout the life of a parasite is particularly challenging for helminths with complex life cycles. These parasites undergo major morphological changes during their life, and parasitize host species that are immunologically, physiologically, and phylogenetically very different. Here, using 16S amplicon sequencing, we characterize the microbiome of the trematode Coitocaecum parvum across four of its life stages: sporocysts, metacercariae and adults inhabiting (respectively) snails, crustaceans and fish, as well as free-living cercariae. Our results demonstrate that, at each life stage, the parasite possesses a phylogenetically diverse microbiome, distinct from that of its hosts or the external environment. The parasite's microbiome comprises bacterial taxa specific to each life stage in different hosts, as well as a small core set of taxa that persists across the parasite's whole life. The apparent existence of an ontogenetically and vertically transmitted core microbiome is supported by the findings that the diversity and taxonomic composition of the microbiome does not vary significantly among life stages, and that the main source of microbial taxa at any life stage is the previous life stage. Our results suggest that microbes are an integrated component of the trematode, possibly shaping its phenotype and host-parasite interactions.
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Affiliation(s)
- Fátima Jorge
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
- Unité Génétique Virale de Biosécurité, Laboratoire de Ploufragan-Plouzané, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Ploufragan, France
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
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176
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Brüssow H. The relationship between the host genome, microbiome, and host phenotype. Environ Microbiol 2020; 22:1170-1173. [PMID: 32048398 DOI: 10.1111/1462-2920.14938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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177
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Mueller EA, Wisnoski NI, Peralta AL, Lennon JT. Microbial rescue effects: How microbiomes can save hosts from extinction. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13493] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Jay T. Lennon
- Department of Biology Indiana University Bloomington IN USA
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